In this study, we propose a method for downscaling ecological footprint (EF) and biocapacity (BC) to a 1-km square resolution for a spatially flexible analysis of environmental burden balance. To conduct EF downscaling (by land type and consumption category) for all terrestrial areas of Japan, the grid population was multiplied by the scaled EF per capita based on the consumption expenditures and income statistics available at the municipal level. The BC of each land type was estimated following the land-use map. Subsequently, a balance analysis between EF and BC showed the spatial distribution of EF, BC, and the environmental load excess ratio (EF/BC). The values of the environmental load excess ratio significantly varied between grids, and the spatial distributions differed depending on the land type. An example of multiscale balance analysis at municipal and prefectural scales by the developed dataset showed the different distributions of the environmental load excess ratio due to the scale of spatial boundaries and demonstrated its contribution to designing interregional cooperative policies from a multilayered perspective. The established high-resolution dataset can be utilized practically for flexibly analyzing the multilayered spatial boundaries to fill the scale mismatch between natural resources and administrative boundaries. The downscaling method proposed in this study can be applied beyond Japan if similar sets of statistics and land-use information are available, which will significantly improve the spatial resolution of the analysis.